The accuracy and validity are the most important aspects in auto focusing system using image processing. If the focusing window is too big or small, there will be incorrect focus result because of too much background image in the window and complicated computation or object deviating the window. Further study on the choice of the focusing window is carried out and an innovative method solving the above problem efficiently is proposed. Un-uniform sampling is introduced in order to get higher resolution in central part of image and wider view field and make sure that the object is located in the focusing window and the negative effect of the background image is decreased. In addition, sampling parameters are further studied for better performance. The experimental results indicate that the veracity and the validity of focus are improved efficiently and the focusing time is not affected.